A diagnostic model for distinguishing between active tuberculosis and latent tuberculosis infection based on the blood expression profiles of autophagy-related genes.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38131281", "kind": "science-record", "revision": 2, "content_hash": "sha256:6e2e761cb107ea17282caf8a171855f5c3d57b8614448a5dcabc07b3037c8ee1", "created_at": "2026-11-01T19:20:03Z", "updated_at": "2026-11-01T21:32:11Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A diagnostic model for distinguishing between active tuberculosis and latent tuberculosis infection based on the blood expression profiles of autophagy-related genes.", "doi": "10.1177/17534666231217798", "pmid": "38131281", "authors": ["Chengbin Wang", "Jie Hua", "Xiaopu He", "Liang Chen", "Shuhan Lv"], "journal": "Therapeutic advances in respiratory disease", "year": 2023, "abstract": "BACKGROUND: Autophagy is closely involved in the control of mycobacterial infection.\nOBJECTIVES: Here, a diagnostic model was developed using the levels of autophagy-related genes (ARGs) in the blood to differentiate active tuberculosis (ATB) and latent tuberculosis infection (LTBI).\nDESIGN: Secondary data analysis of three prospective cohorts.\nMETHODS: The expression of ARGs in patients with ATB and LTBI were analyzed using the GSE37250, GSE19491, and GSE28623 datasets from the GEO database.\nRESULTS: Twenty-two differentially expressed ARGs were identified in the training dataset GSE37250. Using least absolute shrinkage and selection operator and multivariate logistic regression, three ARGs (FOXO1, CCL2, and ITGA3) were found that were positively associated with adaptive immune-related lymphocytes and negatively associated with myeloid and inflammatory cells. A nomogram was constructed using the three ARGs. The accuracy, consistency, and clinical relevance of the nomogram were evaluated using receiver operating characteristic curves, the C-index, calibration curves, and validation in the datasets GSE19491 and GSE28623. The nomogram showed good predictive performance.\nCONCLUSION: The nomogram was able to accurately differentiate between ATB and LTBI patients. These findings provide evidence for future study on the pathology of autophagy in tuberculosis infection.", "claims": [{"id": "claim-method", "statement": "Using least absolute shrinkage and selection operator and multivariate logistic regression, three ARGs (FOXO1, CCL2, and ITGA3) were found that were positively associated with adaptive immune-related lymphocytes and negatively associated with myeloid and inflammatory cells.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38131281", "locator": "sections[0] \"Abstract\" paragraph 5", "quote": "Using least absolute shrinkage and selection operator and multivariate logistic regression, three ARGs (FOXO1, CCL2, and ITGA3) were found that were positively associated with adaptive immune-related lymphocytes and negatively associated with myeloid and inflammatory cells."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Availability of data and materials: Publicly available datasets were analyzed in this study. These data can be found in GSE37250 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37250), GSE19491 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19491), and GSE28623 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28623).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38131281", "locator": "sections[21] \"Declarations\" paragraph 1", "quote": "Availability of data and materials: Publicly available datasets were analyzed in this study. These data can be found in GSE37250 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37250), GSE19491 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19491), and GSE28623 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28623)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The nomogram was able to accurately differentiate between ATB and LTBI patients.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38131281", "locator": "sections[0] \"Abstract\" paragraph 6", "quote": "The nomogram was able to accurately differentiate between ATB and LTBI patients."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The nomogram was able to accurately differentiate between ATB and LTBI patients.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:38131281"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE19491"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE19491"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38131281", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1177/17534666231217798", "sha256": "sha256:c962271feaf5b8b263d43b9b8dc6d57a3947f1f6c31ce36e24be23aa3ef67c3a", "bytes": 42006, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1177/17534666231217798", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10748544", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE19491", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19491", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19491", "version": null, "note": "Availability of data and materials: Publicly available datasets were analyzed in this study. These data can be found in GSE37250 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37250), GSE19491 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19491), and GSE28623 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28623).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Availability of data and materials: Publicly available datasets were analyzed in this study. 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These data can be found in GSE37250 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37250), GSE19491 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19491), and GSE28623 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28623).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Availability of data and materials: Publicly available datasets were analyzed in this study. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE37250", "GSE19491", "GSE28623"], "resolved_accessions": ["GSE37250", "GSE19491", "GSE28623"], "statements": ["Availability of data and materials: Publicly available datasets were analyzed in this study. These data can be found in GSE37250 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37250), GSE19491 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19491), and GSE28623 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28623)."], "basis": "The paper names GSE37250, GSE19491, GSE28623 in National Center for Biotechnology Information-Gene Expression Omnibus (NCBI-GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["glm_logit_fit"], "assets": ["source:pmid:38131281", "data:geo:GSE19491"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE19491"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:03:23Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11749, "completion_tokens": 1568, "cached_tokens": 128}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:38131281", "type": "paper", "label": "pmid:38131281"}, {"id": "source:pmid:38131281", "type": "manuscript", "label": "PMID 38131281 full text"}, {"id": "data:geo:GSE19491", "type": "dataset", "label": "GEO GSE19491"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38131281", "type": "paper", "label": "pmid:38131281"}, {"id": "source:pmid:38131281", "type": "manuscript", "label": "PMID 38131281 full text"}, {"id": "data:geo:GSE19491", "type": "dataset", "label": "GEO GSE19491"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38131281", "type": "extraction", "used": ["source:pmid:38131281"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE19491", "type": "accession_resolution", "used": ["data:geo:GSE19491"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:38131281", "parent_hash": "sha256:b018fd43279745e39e3f63e1d1f126a149e8bfcc58be09e134c85a995474fe14", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE19491 licence not read", "asset:data:geo:GSE19491 not downloaded", "asset:data:geo:GSE28623 licence not read", "asset:data:geo:GSE28623 not downloaded", "asset:data:geo:GSE37250 licence not read", "asset:data:geo:GSE37250 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "regression_modelling", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["glm_logit_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Using least absolute shrinkage and selection operator and multivariate logistic regression, three ARGs (FOXO1, CCL2, and ITGA3) were found that were positively associated with adaptive immune-related lymphocytes and negatively associated with myeloid and inflammatory cells."], "order_basis": "analysis_only", "id": "assay:1"}]}